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http://brainblogger.com/

With a team of over 80 contributors, this award winning collaborative health and science blog covers topics from multidimensional biopsychosocial perspectives. We review the most impactful news and research related to neuroscience / neurology, psychology / psychiatry, and health / healthcare. Our blog serves as a beacon for attracting new minds beyond the basic sciences of brain and into the biopsychosocial model. Founded in 2005 by Dr. Shaheen Lakhan, Brain Blogger is an official undertaking of the Global Neuroscience Initiative Foundation (GNIF) an international charity for the advancement of neurological and mental health patient welfare, education, and research. Brain Blogger is one of the most effective mediums for the GNIF to raise awareness of neuro-related topics. We are a proud member of the 9rules Network and the Scientific American Partner Network a handful of selected blogs that share similar interests and readership. Also, our commitment to ethical biomedical journalism is exemplified by successfully undergoing annual voluntary certification by HONcode the oldest and the most used ethical and trustworthy code for medical and health related information available on internet. Moreover, we are a member of the Healthcare Blogger Code of Ethics. Under the editorship of Dr. Shaheen Lakhan, Brain Blogger hosts a team of over 80 contributors from diverse academic, professional, and social backgrounds: including neurosurgeons (Dr. McCleary), psychotherapists (Mr. Yourell), forensic psychologists (Dr. MacHovec), registered nurses (Mrs. Jones), clinical pharmacists (Dr. Gibson), patient advocates (Mrs. Wilson-Herndon), and general citizens concerned about neurological and mental health (Mr. McIntyre). To join our team, please follow the simple instructions to sign-up online.

Proper citation: Brain Blogger (RRID:SCR_005464) Copy   

•   Source: SciCrunch Registry
  

https://github.com/richardmleggett/nextclip/

A software tool for analysing reads from Long Mate Pair (LMP) libraries, generating a comprehensive quality report and extracting good quality trimmed and deduplicated reads.

Proper citation: NextClip (RRID:SCR_005465) Copy   

•   Source: SciCrunch Registry
  

http://ucneuroscience.com/

Leading treatment, research and teaching center for complex neurological conditions based at the University Hospital and the UC College of Medicine. Its physicians and researchers have created national models for evidence-based treatment and research of complex conditions, including ischemic and hemorrhagic stroke, brain aneurysms, brain and spinal cord trauma, brain tumors, Parkinson's disease, epilepsy and seizure disorders, multiple sclerosis, trigeminal neuralgia, Alzheimer's disease and memory disorders, mood disorders, and neuromuscular disorders. UCNI includes a team of more than 100 experts from 15 specialties who collaborate across disciplines to provide the most comprehensive diagnoses and treatments possible.

Proper citation: University of Cincinnati Neuroscience Institute (RRID:SCR_005345) Copy   

•   Source: SciCrunch Registry
  

http://www.nipgr.res.in/ngsqctoolkit.html

A software toolkit for the quality control (QC) of next generation sequencing (NGS) data. The toolkit comprises of user-friendly stand alone tools for quality control of the sequence data generated using Illumina and Roche 454 platforms with detailed results in the form of tables and graphs, and filtering of high-quality sequence data. It also includes few other tools, which are helpful in NGS data quality control and analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: NGS QC Toolkit (RRID:SCR_005461) Copy   

•   Source: SciCrunch Registry
  

https://github.com/ruping/Breakpointer

A fast tool for locating sequence breakpoints from the alignment of single end reads (SE) produced by next generation sequencing (NGS). It adopts a heuristic method in searching for local mapping signatures created by insertion/deletions (indels) or more complex structural variants(SVs). With current NGS single-end sequencing data, the output regions by Breakpoint mainly contain the approximate breakpoints of indels and a limited number of large SVs. Notably, Breakpointer can uncover breakpoints of insertions which are longer than the read length. Breakpointer also can find breakpoints of many variants located in repetitive regions. The regions can be used not only as a extra support for SV predictions by other tools (such as by split-read method), but also can serve as a database for searching variants which might be missed by other tools. Breakpointer is a command line tool that runs under linux system. Breakpointer takes advanage of two local mapping features of single-end reads as a consequence of indel/SVs: 1) non-uniform read distribution (depth skewness) and 2) misalignments at the boundaries of indel/SVs. These features are summarized as breakpoint signature. Breakpointer proceeds in three stages in capturing this signature. It is implemented in C++ and perl. Input is the file or files containing alignments of single-end reads against a reference genome (in .BAM format). Output is the predicted regions containing potential breakpoints of SVs (in .GFF format). To be able to read in .BAM files, Breakpointer requires bamtools API, which users should install beforehand.

Proper citation: Breakpointer (RRID:SCR_005254) Copy   

•   Source: SciCrunch Registry
  

https://code.google.com/p/clever-sv/

A collection of tools to discover and genotype structural variations in genomes from paired-end sequencing reads. The main software is written in C++ with some auxiliary scripts in Python.

Proper citation: CLEVER Toolkit (RRID:SCR_005255) Copy   

•   Source: SciCrunch Registry
  

http://research.cs.wisc.edu/wham/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. High-throughput sequence alignment tool that aligns short DNA sequences (reads) to the whole human genome at a rate of over 1500 million 60bps reads per hour, which is one to two orders of magnitudes faster than the leading state-of-the-art techniques. Feature list for the current version (v 0.1.5) of WHAM: * Supports paired-end reads * Supports up to 5 errores * Supports alignments with gaps * Supports quality scores for filtering invalid alignments, and sorting valid alignments * finds ALL valid alignments * Supports multi-threading * Supports rich reporting modes * Supports SAM format output

Proper citation: WHAM (RRID:SCR_005497) Copy   

•   Source: SciCrunch Registry
  

https://code.google.com/p/clippers/

A software program designed to identify long deletions of a genome as well as the RNA splicings using long Illumina reads. Currently, Clippers is implemented for long reads Illumina, ex: 75bp or 100bp, allowing mismatches and a single deletion/splicing. Clippers is a sister tool of PerM, our short reads aligner. Users are strongly suggested to use PerM to initially mapped reads and identify the deletion/splicing with the initially unmapped reads. We plan to extend it to ABI SOLiD reads in the near future. Clippers outputs gap-alignments in SAM format. You can use SAMtools or other program to interpret the deletion/splicing. The input files are a reference in fasta format and the reads is in fasta or fastq format.

Proper citation: Clippers (RRID:SCR_005256) Copy   

•   Source: SciCrunch Registry
  

http://mfiers.github.io/Moa/

Software to assist a bioinformatician to organize, document, share, execute and repeat workflows in a command line environment without losing any of the flexibility of the command line, and, at all times giving the user full access to all aspects of the workflow.

Proper citation: Moa (RRID:SCR_005373) Copy   

•   Source: SciCrunch Registry
  

http://sv.gersteinlab.org/age/

A tool that implements an algorithm for optimal alignment of sequences with Structural Variations (SVs).

Proper citation: AGE (RRID:SCR_005253) Copy   

•   Source: SciCrunch Registry
  

https://rx.uga.edu/academic-programs/master-of-science/pharmaceutical-and-biomedical-sciences/

Department of Pharmaceutical and Biomedical Sciences research focus is on the cutting edge of pharmaceutical sciences. Provides training at professional, master, doctoral and post-doctoral levels in wide range of disciplines, including medicinal chemistry, pharmaceutics, toxicology, drug delivery, pharmacology and many other related biomedical sciences.

Proper citation: University of Georgia College of Pharmacy, Department of Pharmaceutical and Biomedical Sciences (RRID:SCR_005374) Copy   

•   Source: SciCrunch Registry
  

http://www-personal.umich.edu/~jianghui/seqmap/

A software tool for mapping large amount of oligonucleotide to the genome. It is designed for finding all the places in a genome where an oligonucleotide could potentially come from. SeqMap can efficiently map as many as dozens of millions of short sequences to a genome of several billions of nucleotides. While doing the mapping, several mutations as well as insertions / deletions of the nucleotide bases in the sequences can be tolerated and furthermore detected. Various input and output formats are supported, as well as many command line options for tuning almost every steps in the mapping process. A typical mapping can be done in a few hours on an ordinary PC.

Proper citation: SeqMap (RRID:SCR_005495) Copy   

•   Source: SciCrunch Registry
  

http://www.genome.umd.edu/jellyfish.html

A software tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers quickly by using an efficient encoding of a hash table and by exploiting the compare-and-swap CPU instruction to increase parallelism. Jellyfish is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the jellyfish dump command., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Jellyfish (RRID:SCR_005491) Copy   

•   Source: SciCrunch Registry
  

https://github.com/mfumagalli/ngsTools

A collection of software programs for population genetics analyses from NGS (Next-Generation Sequencing) data, taking into account its statistical uncertainty. The methods implemented in these programs do not rely on SNP (Single Nucleotide Polymorphism) or genotype calling, and are particularly suitable for low sequencing depth data.

Proper citation: ngsTools (RRID:SCR_005489) Copy   

•   Source: SciCrunch Registry
  

http://openbiobank.com/

This is a demo store. Any orders placed through this store will not be honored or fulfilled. The Open Biobank is a network of bio-banks, collaborators, and consumers supplying or acquiring samples that are proactively acquired for future testing, analysis, and/or replenishment for human life. Our goal is to supply quality samples to clinicians and researchers with making their ordering experience convenient, accessible, and available 24/7. Suppliers that we distribute for are Bio-Banks, Tissues Banks, and Seed Banks who supply samples to the open life science community. Samples are stored in bio-repositories, physical and data storage facilities with various controlled environments normally containing associated data history on the sample(s) sourced. We have a policy to provide all consumers with documentation from suppliers on the state, procedures, protocols, and historical data on sample handling and testing analysis on samples ordered from suppliers. In choosing samples to order, suppliers categorize the usage, handling, environment, and application of samples to properly supply samples to users. However, users expect information on sample handling, collection or harvesting, storage, management, shipment, and other logistical considerations that may affect sample quality and impact sample use. The Amazon-like storefront saves lives by sourcing samples from all bio-banks around the world. This is how it works: * Choose a supplier you trust. Find the sample you need. Select samples from search results and place an order. Payment systems by Amazon are reliable. Choose your shipper and method of delivery. Track your orders from multiple vendors. Query reports of all orders place by your staff. Rate the samples you ordered and view the ratings of your peers. * Market your Biospecimen and Data on the Open Biobank

Proper citation: Open Biobank (RRID:SCR_005364) Copy   

•   Source: SciCrunch Registry
  

http://www.tgen.org/news/index.cfm?pageid=842

Podcasts (Audio and video files over the internet) form the Translational Genomics Research Institute.

Proper citation: TGen Podcasts (RRID:SCR_005365) Copy   

•   Source: SciCrunch Registry
  

http://mrfast.sourceforge.net/

Software designed to map short reads generated with the Illumina platform to reference genome assemblies; in a fast and memory-efficient mannerl. Currently Supported Features: * Output in SAM format * Indels up to 8 bp (4 bp deletions and 4 bp insertions) * Paired-end mapping ** Discordant option to generate mapping file ready for VariationHunter to detect structural variants. * One end anchored (OEA) map locations for novel sequence insertion detection with NovelSeq * Matepair library mapping (long inserts with RF orientation). Planned Features: * Multithreading

Proper citation: mrFAST (RRID:SCR_005487) Copy   

•   Source: SciCrunch Registry
  

http://dna.cs.byu.edu/gnumap/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 3rd,2023. A software program designed to accurately map sequence data obtained from next-generation sequencing machines (specifically that of Solexa/Illumina) back to a genome of any size. By using the posterior probability of mapping a given read to a specific genomic loation, we are able to account for repetitive reads by distributing them across several regions in the genome. In addition, the output of the program is created in such a way that it can be easily viewed through other free and readily- available programs. Several benchmark data sets were created with spiked-in duplicate regions, and GNUMAP was able to more accurately account for these duplicate regions.

Proper citation: GNUMAP (RRID:SCR_005482) Copy   

•   Source: SciCrunch Registry
  

http://fcon_1000.projects.nitrc.org/fcpClassic/FcpTable.html

1200+ ''resting state'' functional MRI (R-fMRI) datasets independently collected at 33 sites and donated by the principal investigators for the purpose of providing the broader imaging community complete access to a large-scale functional imaging dataset. Age, sex and imaging center information are provided for each of the datasets. In accordance with HIPAA guidelines, all datasets are anonymous, with no protected health information included. We anticipate this data-sharing effort will equip researchers with a means of exploring and refining R-fMRI approaches, and facilitate the growing ethos of sharing and collaboration. Disclaimer: The ''1000 Functional Connectomes Project'' datasets are provided freely without assurance of quality or appropriateness for usage.

Proper citation: FCP Classic Data Sharing Samples (RRID:SCR_005362) Copy   

•   Source: SciCrunch Registry
  

http://www.ebi.ac.uk/research/enright/software/kraken

A set of software tools ( Reaper, Tally and Sequence Imp) designed to streamline the analysis of next-generation sequencing data. Although designed with small RNA sequence analysis in mind the tools can be used to address issues facing next-generation sequencing in general.

Proper citation: Kraken (RRID:SCR_005484) Copy   

•   Source: SciCrunch Registry